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De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production

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ABSTRACT

Background: Microalgae, which can absorb carbon dioxide and then transform it into lipid, are promising candidates to produce renewable energy, especially biodiesel. The paucity of genomic information, however, limits the development of genome-based genetic modification to improve lipid production in many microalgae. Here, we describe the de novo sequencing, transcriptome assembly, annotation and differential expression analysis for Chlorella sorokiniana cultivated in different conditions to reveal the change of genes expression associated with lipid accumulation and photosynthetic carbon fixation.

Results: Six cultivation conditions were selected to cultivate C. sorokiniana. Lipid content of C. sorokiniana under nitrogen-limited condition was 2.96 times than that under nitrogen-replete condition. When cultivated in light with nitrogen-limited supply, C. sorokiniana can use carbon dioxide to accumulate lipid. Then, transcriptome of C. sorokiniana was sequenced using Illumina paired-end sequencing technology, and 244,291,069 raw reads with length of 100 bp were produced. After preprocessed, these reads were de novo assembled into 63,811 contigs among which 23,528 contigs were found homologous sequences in public databases through Blastx. Gene expression abundance under six conditions were quantified by calculating FPKM value. Ultimately, we found 385 genes at least 2-fold up-regulated while 71 genes at least 2-fold down-regulated in nitrogen-limited condition. Also, 204 genes were at least 2-fold up-regulated in light while 638 genes at least 2-fold down-regulated. Finally, 16 genes were selected to conduct RT-qPCR and 15 genes showed the similar results as those identified by transcriptomic analysis in term of differential expression.

Conclusions: De novo transcriptomic analyses have generated enormous information over C. sorokiniana, revealing a broad overview of genomic information related to lipid accumulation and photosynthetic carbon fixation. The genes with expression change under different conditions are highly likely the potential targets for genetic modification to improve lipid production and CO2 fixation efficiency in oleaginous microalgae.

Electronic supplementary material: The online version of this article (doi:10.1186/s12866-016-0839-8) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Growth and lipid content of C. sorokiniana under different conditions. a: Growth and lipid content of C. sorokiniana under nitrogen-limited and nitrogen-replete conditions. b: The consumption of glucose under nitrogen-limited and nitrogen-replete conditions; c: Growth and lipid content of C. sorokiniana in light; d: Growth and lipid content of C. sorokiniana in dark
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Fig1: Growth and lipid content of C. sorokiniana under different conditions. a: Growth and lipid content of C. sorokiniana under nitrogen-limited and nitrogen-replete conditions. b: The consumption of glucose under nitrogen-limited and nitrogen-replete conditions; c: Growth and lipid content of C. sorokiniana in light; d: Growth and lipid content of C. sorokiniana in dark

Mentions: Six different cultivation conditions were selected to culture C. sorokiniana (Table 1), and the growth and lipid content profiles under these conditions were shown in Fig. 1. With 4 % glucose as carbon source, the optical density of the culture at 680 nm (OD680) in nitrogen-limited condition (0.2 % KNO3 supply) was almost equal to that in nitrogen-replete condition (0.8 % KNO3 supply) before 48 h. After 48 h the OD680 in nitrogen-replete condition began to become higher than that in nitrogen-limited condition (Fig. 1a). The higher OD680 resulted in the more glucose consumption (Fig. 1b) for cell growth, not for lipid production. The nitrogen-limited condition could induce C. sorokiniana to accumulate more lipid. After 48 h, the fluorescence intensity of lipid dyed with nile red in nitrogen-limited condition was higher than that in nitrogen-replete condition, meaning that the cells in nitrogen-limited condition accumulated more lipid. At 84 h, The fluorescence intensity in nitrogen-limited condition was as high as 2.96 times than that in nitrogen-replete condition (340 ± 19 and 115 ± 6, respectively Fig. 1a).Table 1


De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production
Growth and lipid content of C. sorokiniana under different conditions. a: Growth and lipid content of C. sorokiniana under nitrogen-limited and nitrogen-replete conditions. b: The consumption of glucose under nitrogen-limited and nitrogen-replete conditions; c: Growth and lipid content of C. sorokiniana in light; d: Growth and lipid content of C. sorokiniana in dark
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5037625&req=5

Fig1: Growth and lipid content of C. sorokiniana under different conditions. a: Growth and lipid content of C. sorokiniana under nitrogen-limited and nitrogen-replete conditions. b: The consumption of glucose under nitrogen-limited and nitrogen-replete conditions; c: Growth and lipid content of C. sorokiniana in light; d: Growth and lipid content of C. sorokiniana in dark
Mentions: Six different cultivation conditions were selected to culture C. sorokiniana (Table 1), and the growth and lipid content profiles under these conditions were shown in Fig. 1. With 4 % glucose as carbon source, the optical density of the culture at 680 nm (OD680) in nitrogen-limited condition (0.2 % KNO3 supply) was almost equal to that in nitrogen-replete condition (0.8 % KNO3 supply) before 48 h. After 48 h the OD680 in nitrogen-replete condition began to become higher than that in nitrogen-limited condition (Fig. 1a). The higher OD680 resulted in the more glucose consumption (Fig. 1b) for cell growth, not for lipid production. The nitrogen-limited condition could induce C. sorokiniana to accumulate more lipid. After 48 h, the fluorescence intensity of lipid dyed with nile red in nitrogen-limited condition was higher than that in nitrogen-replete condition, meaning that the cells in nitrogen-limited condition accumulated more lipid. At 84 h, The fluorescence intensity in nitrogen-limited condition was as high as 2.96 times than that in nitrogen-replete condition (340 ± 19 and 115 ± 6, respectively Fig. 1a).Table 1

View Article: PubMed Central - PubMed

ABSTRACT

Background: Microalgae, which can absorb carbon dioxide and then transform it into lipid, are promising candidates to produce renewable energy, especially biodiesel. The paucity of genomic information, however, limits the development of genome-based genetic modification to improve lipid production in many microalgae. Here, we describe the de novo sequencing, transcriptome assembly, annotation and differential expression analysis for Chlorella sorokiniana cultivated in different conditions to reveal the change of genes expression associated with lipid accumulation and photosynthetic carbon fixation.

Results: Six cultivation conditions were selected to cultivate C. sorokiniana. Lipid content of C. sorokiniana under nitrogen-limited condition was 2.96 times than that under nitrogen-replete condition. When cultivated in light with nitrogen-limited supply, C. sorokiniana can use carbon dioxide to accumulate lipid. Then, transcriptome of C. sorokiniana was sequenced using Illumina paired-end sequencing technology, and 244,291,069 raw reads with length of 100 bp were produced. After preprocessed, these reads were de novo assembled into 63,811 contigs among which 23,528 contigs were found homologous sequences in public databases through Blastx. Gene expression abundance under six conditions were quantified by calculating FPKM value. Ultimately, we found 385 genes at least 2-fold up-regulated while 71 genes at least 2-fold down-regulated in nitrogen-limited condition. Also, 204 genes were at least 2-fold up-regulated in light while 638 genes at least 2-fold down-regulated. Finally, 16 genes were selected to conduct RT-qPCR and 15 genes showed the similar results as those identified by transcriptomic analysis in term of differential expression.

Conclusions: De novo transcriptomic analyses have generated enormous information over C. sorokiniana, revealing a broad overview of genomic information related to lipid accumulation and photosynthetic carbon fixation. The genes with expression change under different conditions are highly likely the potential targets for genetic modification to improve lipid production and CO2 fixation efficiency in oleaginous microalgae.

Electronic supplementary material: The online version of this article (doi:10.1186/s12866-016-0839-8) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus